<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36518?offset=190 https://bioinformaticsonline.com/bookmarks/view/19631/rosalind-bioinformatics-problems Thu, 18 Dec 2014 10:32:48 -0600 https://bioinformaticsonline.com/bookmarks/view/19631/rosalind-bioinformatics-problems <![CDATA[Rosalind Bioinformatics problems !!!]]> Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

http://rosalind.info/problems/list-view/

Address of the bookmark: http://rosalind.info/problems/list-view/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/26993/lastz Mon, 18 Apr 2016 04:41:55 -0500 https://bioinformaticsonline.com/bookmarks/view/26993/lastz <![CDATA[LASTZ]]> LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

More at http://www.bx.psu.edu/~rsharris/lastz/

Thesis: http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf

Address of the bookmark: http://www.bx.psu.edu/~rsharris/lastz/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/23174/scaffolding-of-a-bacterial-genome-using-minion-nanopore-sequencing Tue, 07 Jul 2015 16:59:25 -0500 https://bioinformaticsonline.com/bookmarks/view/23174/scaffolding-of-a-bacterial-genome-using-minion-nanopore-sequencing <![CDATA[Scaffolding of a bacterial genome using MinION nanopore sequencing]]> Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program.

Address of the bookmark: http://www.nature.com/srep/2015/150707/srep11996/full/srep11996.html

]]> Rahul Agarwal https://bioinformaticsonline.com/researchlabs/view/26499/katju-lab Fri, 26 Feb 2016 03:25:32 -0600 <![CDATA[Katju Lab]]> TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes. Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.

http://katjulab.com/research.html

]]> https://bioinformaticsonline.com/bookmarks/view/26306/busco Sun, 07 Feb 2016 16:02:39 -0600 https://bioinformaticsonline.com/bookmarks/view/26306/busco <![CDATA[BUSCO]]> Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/26325/crossmap Mon, 08 Feb 2016 15:47:00 -0600 https://bioinformaticsonline.com/bookmarks/view/26325/crossmap <![CDATA[CrossMap]]> CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)).

It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.

We do not recommend using CrossMap to convert genome coordinates between species.

More at http://crossmap.sourceforge.net/

Address of the bookmark: http://crossmap.sourceforge.net/

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/27110/easyfig Fri, 29 Apr 2016 05:49:39 -0500 https://bioinformaticsonline.com/bookmarks/view/27110/easyfig <![CDATA[Easyfig]]> Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig.  Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

More at http://easyfig.sourceforge.net/

Address of the bookmark: http://easyfig.sourceforge.net/

]]> Poonam Mahapatra https://bioinformaticsonline.com/bookmarks/view/26968/scalce Fri, 15 Apr 2016 05:09:51 -0500 https://bioinformaticsonline.com/bookmarks/view/26968/scalce <![CDATA[SCALCE]]> SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any valid FASTQ with consistent read lengths. 

More at http://sfu-compbio.github.io/scalce/

Address of the bookmark: http://sfu-compbio.github.io/scalce/

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/27035/spades Tue, 19 Apr 2016 08:37:08 -0500 https://bioinformaticsonline.com/bookmarks/view/27035/spades <![CDATA[SPAdes]]> SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau.ru/en/spades.

Manual at http://spades.bioinf.spbau.ru/release3.7.1/manual.html

Address of the bookmark: http://bioinf.spbau.ru/spades

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/27078/homer-software-for-motif-discovery-and-next-gen-sequencing-analysis Tue, 26 Apr 2016 03:48:23 -0500 https://bioinformaticsonline.com/bookmarks/view/27078/homer-software-for-motif-discovery-and-next-gen-sequencing-analysis <![CDATA[HOMER: Software for motif discovery and next-gen sequencing analysis]]> This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER.

  1. Setting up your computing environment
  2. Retrieving and storing sequencing files (your own data or from public sources)
  3. Checking sequence quality, trimming, general sequence manipulation
  4. Mapping reads to a reference genome
  5. Manipulating SAM/BAM alignment files
  6. Visualizing data in a genome browser


RNA-Seq

  1. De novo transcript discovery and differential analysis with Cufflinks
  2. Differential expression analysis with R/Bioconductor
  3. Clustering of large expression datasets (microarray or RNA-Seq)


Microarray

  1. Basic analysis of Affymetrix Gene Expression Arrays using R/Bioconductor

General Tips for Data Analysis

  1. Excel workarounds, adding gene annotation, X-Y plots tips, etc.

Address of the bookmark: http://homer.salk.edu/homer/basicTutorial/

]]> Neel